Package: RTCGAToolbox 2.43.0

Marcel Ramos

RTCGAToolbox: A new tool for exporting TCGA Firehose data

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

Authors:Mehmet Samur [aut], Marcel Ramos [aut, cre], Ludwig Geistlinger [ctb]

RTCGAToolbox_2.43.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RTCGAToolbox/json (API)

# Install 'RTCGAToolbox' in R:

install.packages('RTCGAToolbox', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mksamur/rtcgatoolbox/issues

Datasets:

accmini - A subset of the Adrenocortical Carcinoma (ACC) dataset

On BioConductor:RTCGAToolbox-2.43.0(bioc 3.24)RTCGAToolbox-2.42.0(bioc 3.23)

differentialexpression geneexpression sequencing

9.70 score 19 stars 5 packages 106 scripts 22 mentions 15 exports 97 dependencies

Last updated from:7e5f79d748. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	280
linux-devel-x86_64	OK	483
source / vignettes	OK	367
linux-release-x86_64	OK	410
macos-release-arm64	OK	256
macos-oldrel-arm64	OK	218
windows-devel	OK	483
windows-release	OK	455
windows-oldrel	OK	445
wasm-release	OK	234

Exports:biocExtract getBroadSubtypes getData getFirehoseAnalyzeDates getFirehoseData getFirehoseDatasets getFirehoseRunningDates getGISTICPeaks getLinks getMutationRate isEmpty makeSummarizedExperimentFromGISTIC selectType showResults updateObject

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI DelayedArray dplyr fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicDataCommons GenomicFeatures GenomicRanges glue hms httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment openssl pillar pkgconfig png prettyunits progress purrr R6 RaggedExperiment rappdirs RCurl readr restfulr Rhtslib rjson RJSONIO rlang Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors selectr Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys TCGAutils tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XML xml2 XVector yaml

RTCGAToolbox

Rendered fromRTCGAToolbox-vignette.Rmdusingknitr::rmarkdown

Last update: 2020-10-09
Started: 2015-03-31

Help page	Topics
A subset of the Adrenocortical Carcinoma (ACC) dataset	accmini
Extract and convert data from a 'FirehoseData' object to a 'Bioconductor' object	biocExtract
An S4 class to store correlations between gene expression level and copy number data	CorResult-class
An S4 class to store differential gene expression results	DGEResult-class
An S4 class to store data from CGA platforms	FirehoseCGHArray-class
An S4 class to store main data object from clinent function.	FirehoseData-class getData,ANY-method getData,FirehoseData-method getData,FirehoseGISTIC-method selectType,FirehoseData-method show,FirehoseData-method updateObject,FirehoseData-method
An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)	FirehoseGISTIC-class isEmpty,FirehoseGISTIC-method updateObject,FirehoseGISTIC-method
An S4 class to store data from methylation platforms	FirehoseMethylationArray-class
An S4 class to store data from array (mRNA, miRNA etc.) platforms	FirehosemRNAArray-class
Download expression-based cancer subtypes from the Broad Institute	getBroadSubtypes
Extract data from FirehoseData object	getData
Get data analyze dates.	getFirehoseAnalyzeDates
Get data from Firehose portal.	getFirehoseData
Get a list of TCGA disease cohorts	getFirehoseDatasets
Get standard data running dates.	getFirehoseRunningDates
Download GISTIC2 peak-level data from the Firehose pipeline	getGISTICPeaks
Get resource links from inputs	getLinks
Make a table for mutation rate of each gene in the cohort	getMutationRate
Gene coordinates for circle plot.	hg19.ucsc.gene.locations
Create a SummarizedExperiment from FireHose GISTIC	makeSummarizedExperimentFromGISTIC
RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data	RTCGAToolbox-package RTCGAToolbox
Accessor function for the FirehoseData object	selectType
Export toptable or correlation data frame	showResults
Export toptable or correlation data frame	showResults,CorResult,CorResult-method showResults,CorResult-method
Export toptable or correlation data frame	showResults,DGEResult,DGEResult-method showResults,DGEResult-method

Package: RTCGAToolbox 2.43.0

RTCGAToolbox: A new tool for exporting TCGA Firehose data

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